Why are two collections of identical rigid bodies simulated differently?
In general, rigid body simulations are not perfectly deterministic. The more complex they are, the more influence the small but unavoidable numerical imprecisions have. You might be able to duplicate simple simulations somewhat reliably, but increasing complexity will mean increasing difference in results between simulation runs.
Therefore, if you want perfectly identical behavior, you will need to bake the dynamics (quite possibly it would be best to bake to keyframes in this circumstances) before duplicating the bodies.